taxaResolve: Resolve taxonmic names online

In treeman: Phylogenetic Tree Manipulation Class and Methods

Description

Resolve taxonomic names via the Global Names Resolver.

Usage

taxaResolve(
  nms,
  batch = 100,
  datasource = 4,
  genus = TRUE,
  cache = FALSE,
  parent = NULL
)

Arguments

nms	vector of names
batch	size of the batches to be queried
datasource	ID number of the datasource
genus	boolean, if true will search against GNR with just the genus name for names that failed to resolve using the full species name
cache	T/F, create a local cache of downloaded names?
parent	specify parent of all names to prevent false names

Details

Returns dataframe containing GNR metadata for each name wames that cannot be resolved are returned as NA. Various datasources are available, see http://resolver.globalnames.org/data_sources for a list and IDs. Default is 4 for NCBI. Will raise a warning if connection fails and will return NULL.

See Also

searchTxnyms, setTxnyms, getNdsFrmTxnyms

Examples

my_lovely_names <- c ('Gallus gallus', 'Pongo pingu', 'Homo sapiens',
                      'Arabidopsis thaliana', 'Macaca thibetana', 'Bacillus subtilis')
res <- taxaResolve (nms=my_lovely_names)
length(colnames(res))  # 10 different metadata for returned names including original search name
# let's look at the lineages
lineages <- strsplit(as.vector(res$lineage), '\\|')
print(lineages[[6]])  # the bacteria has far fewer taxonomic levels

treeman documentation built on July 8, 2020, 7:28 p.m.